PRODORIC: state-of-the-art database of prokaryotic gene regulation

Area of Science:

• Genomics and Bioinformatics
• Molecular Biology
• Computational Biology

Background:

• PRODORIC is a major repository for prokaryotic transcription factor binding sites.
• Previous versions established web interfaces and visualization tools.
• The need for improved data accessibility and quality was identified.

Purpose of the Study:

• To release an updated version of the PRODORIC database with enhanced features and data.
• To provide programmatic access to the complete PRODORIC dataset via an API.
• To improve the overall quality and comprehensiveness of the transcription factor binding site information.

Main Methods:

• Transitioned the database backend to a fully API-based architecture.
• Reannotated the entire PRODORIC dataset, re-evaluating each transcription factor binding site.
• Integrated original visualization tools (Genome Browser, ProdoNet) and reintroduced Virtual Footprint functionalities.
• Added new parameters for transcription factors, including bound effectors and regulation types.

Main Results:

• The PRODORIC database backend is now fully API-based, enabling programmatic data access.
• The dataset was reannotated, significantly increasing overall database quality.
• 109 new transcription factors and 6 new organisms were added.
• Enhanced visualization tools and input/output options are now available on the website.

Conclusions:

• The latest PRODORIC release provides a robust, API-driven platform for accessing and analyzing prokaryotic transcription factor binding site data.
• The enhanced data quality and expanded content improve its utility for researchers in bacterial genomics and gene regulation.
• PRODORIC continues to be a valuable resource for the scientific community, now with improved accessibility and functionality.